Stanton thinks he first hurt his calf last Thursday, when he was hit by a pitch near his left knee during live batting practice. That session preceded his rehab-game debut with the High-A Tampa Tarpons on Monday.
"It's hard to pin down exactly what happened," Boone said. "In talking to G, he feels like it's a result of that [the hit-by-pitch]. It's where he got hit on the knee/calf. So not sure exactly, but that's kind of his feeling on what happened."
Stanton, who homered in Monday's game, was scratched from his game with the Tarpons on Tuesday.
Boone said Tuesday night after the Yankees' game in Baltimore that the scratch was "precautionary." He said Stanton had discomfort in his left calf/knee area but was expected back in the lineup Wednesday.
The Yankees announced Wednesday that Stanton, who has been on the 10-day injured list since April 1 because of biceps and shoulder injuries, has been returned to the IL, meaning the club can reset his minor league rehab window.
Boone said that despite the setback, "There's a lot of season left for [Stanton] to impact."
"Good news is at least it seems somewhat minor in the grand scheme of things," Boone said. "Obviously we want G back, and I know he wants to be here -- yesterday. It's a bump in the road, but hopefully it's not something that keeps him down very long, and he gets ramped back up. Once he's cleared again, it should go very quickly."
ESPN's Coley Harvey contributed to this report.